Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors

Miaomiao Li, Tao Yao, Wanru Lin, Will E. Hinckley, Mary Galli, Wellington Muchero, Andrea Gallavotti, Jin-Gui Chen and Shao-shan Carol Huang ()
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Miaomiao Li: New York University
Tao Yao: Oak Ridge National Laboratory
Wanru Lin: New York University
Will E. Hinckley: New York University
Mary Galli: Rutgers University
Wellington Muchero: Oak Ridge National Laboratory
Andrea Gallavotti: Rutgers University
Jin-Gui Chen: Oak Ridge National Laboratory
Shao-shan Carol Huang: New York University

Nature Communications, 2023, vol. 14, issue 1, 1-19

Abstract: Abstract Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. Dimerization of BASIC LEUCINE ZIPPER (bZIP) TFs are critical for their functions, but the molecular mechanism underlying the DNA binding and functional specificity of homo- versus heterodimers remains elusive. To address this gap, we present the double DNA Affinity Purification-sequencing (dDAP-seq) technique that maps heterodimer binding sites on endogenous genomic DNA. Using dDAP-seq we profile twenty pairs of C/S1 bZIP heterodimers and S1 homodimers in Arabidopsis and show that heterodimerization significantly expands the DNA binding preferences of these TFs. Analysis of dDAP-seq binding sites reveals the function of bZIP9 in abscisic acid response and the role of bZIP53 heterodimer-specific binding in seed maturation. The C/S1 heterodimers show distinct preferences for the ACGT elements recognized by plant bZIPs and motifs resembling the yeast GCN4 cis-elements. This study demonstrates the potential of dDAP-seq in deciphering the DNA binding specificities of interacting TFs that are key for combinatorial gene regulation.

Date: 2023
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DOI: 10.1038/s41467-023-38096-2

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